est_paras: A function harmonising datasets and estimate background...

In YangLabHKUST/MR-APSS: The MRAPSS package implement the MR-APPSS approach to test for the causal effect of an exposure on a outcome disease.

A function harmonising datasets and estimate background parameters by LD score regression.

Description

A function harmonising datasets and estimate background parameters by LD score regression.

Usage

est_paras(
  dat1,
  dat2,
  trait1.name = "exposure",
  trait2.name = "outcome",
  LDSC = T,
  h2.fix.intercept = F,
  ldscore.dir = NULLL
)

Arguments

dat1:	formmated summary statistics for trait 1.
dat2:	formmated summary statistics for trait 2.
trait1.name:	specify the name of trait 1, default 'exposure'.
trait2.name:	specify the name of trait 2, default 'outcome'.
LDSC:	whether to run LD score regression, default 'TRUE'. If 'FALSE', the function will not give the parameter estimates but will do harmonising.
h2.fix.intercept:	whether to fix LD score regression intercept to 1, default 'FALSE'.
ldscore.dir:	specify the path to the LD score files.

Value

List with the following elements:

Mdat

Homonised data set

C

the estimated C matrix capturing the effects of sample structure

Omega

the estimated variance-covariance matrix for polygenic effects

YangLabHKUST/MR-APSS documentation built on April 13, 2025, 7:56 p.m.